WHO s code of conduct for open and timely sharing of pathogen genetic sequence data during outbreaks of infectious disease

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Poppy Ray
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1 WHO s code of conduct for open and timely sharing of pathogen genetic sequence data during outbreaks of infectious disease According to WHOs 2016 guidance on managing ethical issues in outbreaks 1, rapid data sharing is critical during an unfolding health emergency. The ethically appropriate and rapid sharing of data can help identify etiological factors, predict disease spread, evaluate existing and novel treatments, symptomatic care and preventive measures, and guide the deployment of limited resources. Pathogen genetic sequence data (GSD) is an increasingly valuable source of information in understanding and controlling outbreaks of infectious disease as articulated in a 2017 meeting report of the WHO R&D Blueprint 2. The extensive applications include, for example, identifying the cause of the outbreak, even if by a previously unknown pathogen, better understanding of transmission, validating diagnostics, and developing therapeutics and preventives. With the advent of next generation sequencing, the depth/extent of available information will expand further. A key concern in recent outbreaks has been variable timelines between the start of an outbreak and the public availability of the first and subsequent genetic sequences. While the first sequences are particularly important to identify and confirm the etiological agent, the ongoing public disclosure of GSD as the outbreak develops allows for monitoring of many elements of the response 3. WHO strongly supports public access to sequence data to inform public health and research decision-making during outbreaks, the equitable sharing of benefits derived from the use of such data, and the legitimate interests of data providers. WHO has consulted with many stakeholders and institutions working in the pathogen sequencing arena, including those who have been involved in applications to recent outbreaks. Based on these consultations, and on lessons learned from recent outbreaks as part of the data sharing workstream of the WHO R&D Blueprint, WHO is proposing elements of a code of conduct for GSD sharing in infectious disease outbreaks. Through this code of conduct WHO seeks to contribute towards an enabling environment for sharing of pathogen GSD where equitable benefit sharing and the needs of data providers around the world can be addressed so that rapid international sharing of sequence data can occur consistently, in accord with IHR , allowing public health authorities, product developers and researchers to collaborate more effectively from a position of mutual trust with respect for submitters rights to the information they provide. Recognizing pathogen sequencing as a priority during outbreaks In relation to disease outbreaks, there should be a commitment by all stakeholders and institutions involved to make publicly available full data on pathogen genomes in order to quickly generate open, interpretable, and actionable information. This should be at no additional cost to the country(s) experiencing the outbreak See International Health Regulations (2005), Article Page 1 of 6

2 Timeliness is critical Wherever feasible, sequencing should occur as close to the point of sample collection as possible, to empower local capacity, avoid delays, and reduce risk of sample degradation. When the intensity of an outbreak exceeds local capacity, samples should be shared with groups/institutions with demonstrated capacity to generate and share data quickly. The timeframe for data generation and release should not exceed 21 days from sample receipt, although even greater speed is highly desirable in the context of rapidly evolving outbreaks. Sample export where local capacity is insufficient and cannot be established in a timely manner Sample export in accordance with national laws is still in the local and global public health interest for certain applications where local capacity does not suffice and cannot be established quickly enough. In such cases a material transfer agreement (MTA) should be used protecting the legitimate interests of the originating country including with respect to issues of ownership, intellectual property and access and benefit sharing. In this connection, the WHO R&D Blueprint has developed a MTA capacity building tool 5, currently available as a draft for consultation. In cases where sample export occurs, receiving parties should be chosen based on scientific expertise as well as demonstrated commitment to fostering public access to data and results of analyses conducted with the data, respecting terms of ownership, access and benefit sharing, attribution and acknowledgment as well as commitment to local capacity development. International partners should support local capacity development for critical sequence determination and analyses, as a norm associated with working in a developing country. Early public disclosure of pathogen GSD during each outbreak, followed by journal publication, as agreed under medical journal policies In each new outbreak or new transmission season GSD should be made publicly available using a public access mechanism, including a brief description of the immediate implications for outbreak control and public health. The uploading of publicly accessible sequence data should occur before journal publication as indicated in WHO s 2015 R&D Blueprint data sharing consultation 6, and subsequently confirmed in ICMJE policy 7. In particular the first set of sequences providing crucial information on the pathogen, genotype, lineage, and strain(s) causing the outbreak and which may inform on the origin of the outbreak as well as the choice of diagnostics, therapeutics, and vaccines, should be generated and shared as rapidly as possible. Sharing of corresponding anonymised sample metadata (minimally time and place of collection, ideally with demographic, laboratory, and clinical data) is essential to enhance the interpretation and the value of genomic data. Representatives from leading biomedical journals at a WHO R&D Blueprint consultation on data sharing during public health emergencies made an unequivocal assertion that public disclosure of information of relevance to public health emergencies should not be delayed by publication page 9 Page 2 of 6

3 timelines and that early disclosure should not and will not prejudice journal publication of full scientific reports 8. WHO advocates that all medical journals urgently update their policies if necessary so that they actively support pre-publication sharing of pathogen GSD related to outbreaks. Disclaimers preventing publication without coordination with the authors of the original sequence disclosure A common concern is that pre-publication dissemination might allow other scientists to develop publications using such sequence data without involvement of or credit to those who disclosed the original data. One possibility to address this concern is that the providers of the sequence data add a disclaimer notice appended to any disclosure of sequences. A possible template for such a disclaimer is below: 83 DISCLAIMER TEXT; Institutions A &B (from country affected by outbreak) and C &D (international partners) believe in the early sharing of data to support the research and public health response to the outbreak of [name of pathogen or disease]. These data may be downloaded, analysed and used for these purposes. We have released these sequences prior to publication. Our analyses of these sequences is ongoing and a publication is in preparation. It is not permitted to use the sequences for publication ie any type of communication with the general public that describes data generated with the use of the sequences. If you intend to so, you must obtain our permission and coordinate with us This approach has been effectively used in several outbreaks. Publication based on publicly available sequence data prior to publication of the results by the originators without collaboration with those who originally generated the sequences will be considered contrary to this code of conduct. Access to analysis capacity In some settings the main bottleneck to provision of interpretable results from sequencing efforts is the lack of bioinformatics expertise. In some cases sequencing databases can run to terabytes of data, such that raw data transfer and analysis can become a more limiting factor than sequencing itself. An international collaborative model is desirable for development of easy-to-operate, open source algorithms to allow for on-site or cloud-based analysis and interpretation of locally generated sequence data. However until such time as this model is functioning, a network of partners supporting analysis of locally generated data is needed. WHO can assist in establishing such a network Page 3 of 6

4 Incentives Public and philanthropic funders of sequencing initiatives should incentivise groups following the above norms on sequence data access as appropriate. Models for sharing pathogen sequence data Alternative options for publicly accessible pathogen sequence data sharing platforms should be available to serve the needs and preferences in different situations. Where data providers are not concerned about retention of ownership of the data, databases without data access agreements (such as GenBank, ENA and DDBJ) are the default option for sharing. For situations where data providers seek retention of ownership of their data, alternative models with data access agreements (such as GISAID 9 in influenza) have been used to facilitate rapid sharing of GSD. The following elements could be used in such models, with provisions on ownership and access and benefit sharing: 1) A database for hosting pathogen sequence data that meets best practice standards for administration and security 2) A database access agreement in the form of a simple click-through interface that allows providers to share data and allows any genuine individual receiver party ( user ) to access the data in alignment with relevant collaboration principles as outlined in the terms and conditions of the data access agreement, including provisions on ownership, intellectual property and access and benefit sharing. These conditions should include the following elements: allow for ownership of the sequence data to reside with the provider of the data uploaded to the platform; anyone using data accessed from the platform is required to acknowledge/credit/potentially co-author with the providers as appropriate; (secondary) users should, as appropriate, propose and seek to collaborate with the data providers, including joint analysis of data; appropriate intellectual property management 3) A governance mechanism which includes appropriate handling of any conflict of interests and allows for engagement and trust between all parties, including low and middle income countries. This governance mechanism could include the possibility of restricting downloads from the database to those that do not follow required best practices. 4) A dispute resolution mechanism that can mediate where disagreements arise. It is proposed that WHO explore with partners how to establish such mechanisms for sharing GSD for pathogens, and engage in discussions as to where an associated database might be hosted. 9 Global Initiative on Sharing All Influenza Data Page 4 of 6

5 Monitoring and evaluation of this approach The extent to which open, timely, pre-publication sharing of sequence and metadata occurs during outbreaks would be monitored. At the same time, the extent to which principles of equitable benefit sharing and recognition of data providers legitimate interests are honoured should also be evaluated. The success of this approach will depend on its effective functioning as a balanced, credible and equitable system that advances global public health objectives and addresses the legitimate interests of both users and providers of data. 141 Page 5 of 6

6 Table 1: Uses of pathogen sequence data in outbreaks: 1. Characterizing an outbreak pathogen directly or through the identification of the pathogen s common ancestor if it is a novel pathogen; 2. Determining the molecular epidemiology of the pathogen, including its diversity, virulence, transmission routes and timelines, and possible mutation; 3. Identifying hotspots of transmission and helping to pinpoint outbreaks to map where emergency response measures are needed most, 4. Providing clarity on contentious aspects of a given outbreak by specifying the route of transmission within humans and between humans and potential zoonotic reservoirs. This can help target response measures effectively to the most affected or at risk areas, and trace the origin of an outbreak more accurately; 5. Validating and improving molecular diagnostic tool development (i.e. PCR-based assays) based on up to date, relevant genomic data of given pathogen, especially early in the outbreak; 6. Underpin R&D to better understand the immunopathology of the disease, and to identify and/or develop useful interventions (therapeutics and vaccines) for immediate or future outbreak control and prevention; 7. Identify sources and sinks of infections, distinguish locally-transmitted versus imported cases; 8. Improve epidemiological models predicting disease transmission. Longer term benefits: 9. Improving disease surveillance in human and animal hosts. Genome-based surveillance through portable technology can improve diagnostic capabilities in resource-poor (e.g. field) settings, and play a role in detecting outbreaks earlier; 10. Facilitating post emergency research and improving the evidence base of lessons learned. This in turn aids preparedness for the next outbreak, wherever it takes place. Epidemics are not bound by national borders, and sharing GSD from one country allows collaborative exchanges of ideas, products, and expertise which may be beneficial for a similar epidemic in a different country; 11. Monitoring resistance to therapeutics such as antivirals; 12. Allowing the self-correcting nature of science to progress. Initial interpretations of data can be mistaken, and data availability allows replication and peer review. For translational research that leads to public health decisions, a wrong conclusion without prompt correction can slow progress significantly. Page 6 of 6

IMPLEMENTATION OF THE NAGOYA PROTOCOL AND PATHOGEN SHARING: PUBLIC HEALTH IMPLICATIONS

IMPLEMENTATION OF THE NAGOYA PROTOCOL AND PATHOGEN SHARING: PUBLIC HEALTH IMPLICATIONS CBD Distr. GENERAL UNEP/CBD/NP/COP-MOP/2/INF/12 6 December 2015 ENGLISH ONLY CONFERENCE OF THE PARTIES TO THE CONVENTION ON BIOLOGICAL DIVERSITY SERVING AS THE MEETING OF THE PARTIES TO THE NAGOYA PROTOCOL